A wide variety of techniques have been developed to prepare and analyze biological specimens. Example techniques include microscopy, microarray analyses (e.g., protein and nucleic acid microarray analyses), and mass spectrometric methods. Specimens are typically prepared for analysis by applying one or more liquids (e.g., reagents) to the specimens. If a specimen is treated with multiple liquids, both the application and subsequent removal of each liquid can be important for producing stained specimens suitable for analysis. For example, microscope slides bearing biological specimens, e.g., tissue sections or cells, are often treated with a series of manually applied reagents to add color and contrast to otherwise transparent or invisible cells or cell components. This labor-intensive process often results in inconsistent processing due to individual techniques among laboratory technicians and often results in relatively low throughput.
“Dip and dunk” automated machines and automated pipetting systems are often used in laboratories to stain a large number of specimens. Dip and dunk automated machines can process specimens in batches by submerging racks carrying specimen-bearing microscope slides in open baths held in open containers. Unfortunately, carryover of processing liquids between containers leads to contamination and degradation of the processing liquids and inconsistent processing between batches. Worse, cells sloughing off the specimens can cause contamination of other slides in the liquid baths and can lead to misdiagnoses. Dip and dunk processes also utilize excessive volumes of liquids, resulting in relatively high processing costs when the reagents must be changed to reduce the possibility of specimen cross-contamination. The open containers are also prone to evaporative losses and reagent oxidative degradation that may significantly alter the concentration and effectiveness of the reagents, resulting in inconsistent staining characteristics between batches. Additionally, because all the slides in a single rack are dipped into the same baths, each slide is subjected to the same staining protocol, thus preventing individualized specimen processing. Accordingly, dip and dunk automated systems suffer numerous drawbacks. Automated pipetting systems have pipetting heads capable of individually dispensing liquids to specimens. To prevent contamination the pipette tip does not directly contact specimens and may additionally be designed with a disposable tip. To avoid collisions between pipetting heads, automated pipetting systems can be designed with a single pipetting head servicing a set of slides. Unfortunately, the speed of the single pipetting head design limits the systems throughput. Additionally, automated pipetting systems may be designed to dispense relatively small volumes precisely onto specimens in order to reduce the amount of fluid waste generated compared to dip and dunk systems.
Overview of Technology
At least some embodiments are directed to automated specimen processing systems configured to coordinate resources to processes specimen-bearing microscope slides. Algorithms can be used to determine schedules for various tasks to efficiently use the resources and consistently process specimens. In some embodiments, the automated specimen processing system includes movable dispenser apparatuses capable of performing lock cycles for dispensing liquid. The dispenser apparatuses may capable of colliding with one another. Accordingly, the lock cycles can be synchronized to avoid or limit collisions between the dispenser apparatuses and/or interference of the respective functions of the dispenser apparatuses. In one embodiment, an array of dispenser apparatuses can individually process a set of slides in series, parallel, or both, without physically contacting one another. Each dispenser apparatus can include two or more liquid dispensing mechanisms moved based on a dual-lock step protocol. For example, one dispensing mechanism can address slides based on one lock step protocol, and another dispensing mechanism can address the same slides based on another lock step protocol. The lock steps can be synchronized to coordinate movement of the dispensing mechanisms (e.g., dispensing mechanisms capable of colliding) to avoid collisions. The operation of the specimen processing system can also be controlled to avoid collisions between fluidic systems (e.g., staining dispenses, non-staining dispenses, etc.) and other systems, such as material handling components (e.g., slide transfer mechanisms, disposable transfer mechanisms, cover transfer mechanisms, or the like). The various tasks can be scheduled to provide desired throughput while avoiding interferences (including contacts).
The automated specimen processing systems, in some embodiments, include an array of dispenser apparatuses that include robotic pipettors and dispenser heads (e.g., dispenser heads capable of aspirating and dispensing streams of liquids for flooding slides). The pipettors can be positioned above the slides for dispensing, and the dispenser heads can be positioned laterally adjacent the slides for dispensing. In one embodiment, the dispenser heads can have one or two degrees of freedom, and the pipettors can have three degrees of freedom. For example, the dispenser heads can move linearly, and the pipettors can have three directions of linear motion. The robotic pipettors can include, without limitation, robotic arm assemblies configured to aspirate, hold, and dispense liquid.
An automated specimen processing system, in some embodiments, can determine lock steps using algorithms and can select tasks associated with the lock steps. Lock step processing can provide each slide with the same allocation of resources and can provide uniformity of timing or chemistry, or both, across slides for consistent staining, thereby enhancing reliability and repeatability of results. Lock steps can be staggered to prevent collision between moving components capable of physically contacting one another. In some embodiments, multi-lock step processing can include multiple lock steps for applying different liquids with different pipette heads. For example, dual-lock step processing can include two different lock step routines coordinated to provide simultaneous processing of multiple slides or sets of slides using afore described two or more independent liquid dispensing mechanisms. The lock steps can have uniform time durations to provide consistent processing between slides (e.g., slides in the same set, slides in different sets, etc.). The automated specimen processing system can determine collision-free travel paths, time-optimal travel paths, and/or coordinated motion of the robotic components.
At least some embodiments include dual-lock step processes with non-staining lock steps, staining lock steps, or other lock steps. At each non-staining lock step, a dispenser mechanism can be positioned to dispense non-staining liquid (e.g., one or more bulk fluids) onto one slide, or perform an alternative operation such as washing the dispenser. At each staining lock step, another dispenser mechanism can be positioned to dispense liquid (e.g., one or more fresh reagents or other liquids) onto one slide. The non-staining and staining lock steps can be coordinated to concurrently process multiple sets of slides. Additionally, the parameters (e.g., periods of time, order, etc.) of the non-staining lock steps can be different from the parameters (e.g., periods of time, order, etc.) of the staining lock steps. In some embodiments, non-staining lock steps can be repeated at a high frequency to frequently service each slide to, for example, replenish liquids to maintain minimum volumes of liquid on the slides. The staining lock steps can be repeated at a lower frequency because reagents may be applied less frequently. In some embodiments, a single staining lock step is performed for each set of non-staining lock steps. Thus, the dispenser mechanism for dispensing non-staining liquids addresses each slide more often than the staining dispenser mechanism.
In some embodiments, a method for processing specimen-bearing microscope slides held at slide processing stations comprises sequentially addressing the slides with a first dispenser by addressing each slide according to a first lock step. The first dispenser is movable relative to the slide processing stations and is configured deliver liquid onto the addressed slide. The slides are also sequentially addressed by a second dispenser. The second dispenser can addresses each slide according to a second lock step and is movable relative to the slide processing stations. In some embodiments, specimens are individually processed to perform different staining protocols on the specimens. The first lock steps can be scheduled with respect to the second lock steps to prevent any collision between the first and second dispensers while the first and second dispensers sequentially address the slides. After staining and under control from the lock step scheduler, the slides can be robotically transported away from the slide processing stations using, for example, a transport apparatus (e.g., a robotic arm, a transfer mechanism, etc.). The first and second dispensers can be positioned at dispense positions (e.g., next to the slides, above the slides, etc.) addressing and delivering liquid onto the respective slides. As these movements are allocated to a given lock step, they may also be scheduled in order to avoid possible collisions between different transport apparatuses. The operation of the staining stations can also be controlled to avoid interference, including collisions, between the dispensers and the stations when moving slides, handling opposable elements (e.g., covers/arcs for spreading fluid), manipulating liquids on slides, or the like.
An automated specimen processing system, in some embodiments, can include a scheduler module that selects operations and determines the order of the operations to control handling functions (e.g., rack transfer, barcode reading, slide drying, etc.) or other functions with, for example, specific timing requirements. The scheduler module can command components of the system to perform specimen processing, STAT processing of individuals slides or racks, or other types of processing. In some embodiments, the specimen processing system can alternate between different modes of operation depending on whether a user selects STAT processing, target throughput, or other target parameters. The scheduler module, in some embodiments, can include one or more algorithms, databases, and/or staining information. An algorithm can be selected based on, for example, desired staining characteristics, desired processing times, or the like. In some embodiments, one algorithm can be used to generate a schedule for dispensing non-staining liquids (e.g., wash solutions, solvents, deparaffinizing liquids, etc.) and another algorithm can be used to generate a staining schedule for dispensing reagents. Algorithms can also be used to synchronize tasks.
In one mode of operation, the scheduler module queues tasks and executes them in turn each time a resource is available within the context of a given lock step type (e.g., staining, non-staining, etc.). Such resources can include, without limitation, robotic arm assemblies, mixing stations, and other components. In some embodiments, the dual-lock step scheduler module can operate in a job-shop schedule mode of operation, in which tasks are distributed over a resource-time scale to process tasks in a predetermined amount of time. For example, the scheduler module can utilize all available resources at the same time to perform a task in the shortest amount of time. The job-shop schedule mode of operation can be used to devote all resources to a single slide processing station.
Schedules for controlling tasks in the context of specimen processing systems can include, without limitation, tasks for moving components, tasks for dispensing liquids, tasks for operating slide processing stations, tasks for moving items (e.g., racks, slides, opposables, etc.), and so forth. Schedules will run in the context of lock cycles for sequentially executing tasks in order to position dispenser apparatuses relative to slides. For example, a lock cycle can include lock steps for positioning dispenser mechanisms for dispensing liquid onto slides. Schedules for dispensing liquids can include dispense start and stop times. A schedule for operating slide processing stations can include, without limitation, tasks for rolling opposable elements along slides, an incubation task, a vacuum task (e.g., task for applying a vacuum to remove liquid), or the like.
In some embodiments, a method for processing specimen-bearing microscope slides includes delivering the slides to respective slide processing stations, repeatedly performing a first lock cycle that includes sequentially positioning a first dispenser at a plurality of first dispense positions for delivering liquid onto each of the slides, and performing a second lock cycle that includes sequentially positioning a second dispenser at a plurality of second dispense positions for delivering liquid onto each of the slides. Handling of slides can be scheduled to avoid any collisions between material handling components (e.g., slide handlers) when delivering the slides to the respective slide processing stations. The first and second lock cycles are scheduled to prevent any collisions between, for example, the dispensers (e.g., two staining dispensers, two non-staining dispensers, etc.) or other components (e.g., fluidic components, material handling components, slide transfer heads, etc.). In one embodiment, the first lock cycle includes delivering one or more streams of non-staining liquid from the first dispenser, and the second lock cycle includes delivering liquid from one or more robotic pipettors of the second dispenser. The highest frequency lock cycle (i.e., a ‘non-staining’ lock cycle) can be set based on physical limitations of the tasks associated with this lock step (e.g., time required to move bulk fluid robots or other non-staining hardware). The second frequency (i.e., a ‘staining’ lock cycle) can be set to a whole multiple (e.g., 1×, 2×, 3×, etc.) of the highest frequency, and can be selected to accommodate limitations of the tasks associated with this lock step (e.g., time required to aspirate and dispense reagents using staining hardware). In this manner the dual-lock step approach may be adjusted to accommodate various automated specimen processing systems.
In yet further embodiments, a method for processing specimen-bearing microscope slides comprises delivering a first set of specimen-bearing microscope slides to first slide processing stations. A second set of specimen-bearing microscope slides is delivered to second slide processing stations. A non-staining lock cycle is performed and includes moving a first non-staining dispenser sequentially to first dispense positions for dispensing liquid onto slides in the first set and moving a second non-staining dispenser sequentially to second dispense positions for dispensing liquid onto slides in the second set. A staining lock cycle is performed while performing the non-staining lock cycle and includes moving a first staining dispenser sequentially to first reagent dispense positions for dispensing reagent onto slides in the first set and moving a second staining dispenser sequentially to second reagent dispense positions for dispensing reagent onto slides in the second set. The non-staining lock cycle, in some embodiments, can include simultaneously delivering liquid onto pairs of the slides (e.g., one slide in the first set and one slide in the second set) until all the slides have received liquid. In other embodiments, three or more sets of slides can be simultaneously processed by two dispensers, three dispensers, four dispensers, and so forth. The staining lock cycle, in some embodiments, can include dispensing reagent liquid alternatively onto slides in the first set and slides in the second set. In some embodiments, alternatingly dispensing reagent includes (a) delivering reagent onto one of the slides in the first set; (b) after step (a), delivering reagent onto one of the slides in the second set; and (c) sequentially repeating steps (a) and (b) to deliver reagent onto most of or all the slides in the first set and most of or all of the slides in the second set. This process can be repeated to perform a wide range of staining protocols.
In some embodiments, an automated slide processing system includes a plurality of slide processing stations configured to hold respective specimen-bearing microscope slides, a non-staining dispenser apparatus, and a staining dispenser apparatus. The non-staining dispenser apparatus is movable relative to the slide processing stations and configured to sequentially dispense liquid onto the slides. The staining dispenser apparatus is movable relative to the slide processing stations and is configured to sequentially dispense reagent onto each of the slides. The automated slide processing system, in some embodiments, can include a controller in communication with the dispenser apparatuses. The controller can include a computer-readable medium containing instructions for performing a process comprising repeatedly performing lock cycles scheduled to prevent any collisions between the dispenser apparatuses.
At least some embodiments of the technology are directed to a system that contacts specimens with liquid by rolling opposable elements along slides. Distances separating non-planar (e.g., curved) wetted surfaces of the opposable elements and slides carrying the specimens is sufficient to form liquid meniscus layers (e.g., thin fluid films, bands of liquid, etc.) between the wetted surfaces and the slides. For example, a meniscus layer can contact at least a portion of a specimen and can be moved across the slide using manipulative action. Liquid can be dispensed onto the slides to maintain desired volumes of the meniscus layers movable via capillary action. Capillary action can include, without limitation, movement of meniscus layers due to the phenomenon of the liquid spontaneously creeping through a gap between the curved, wetted opposable surface and the slide due to adhesive forces, cohesive forces, and/or surface tension. The opposable element can manipulate (e.g., agitate, displace, etc.) the liquid to process the specimen using relatively small volumes of a liquid to help manage waste and provide consistent processing. Evaporative losses, if any, can be managed by dispensing to maintain a desired volume of liquid, reagent concentration, or the like.